GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pta in Desulfovibrio vulgaris Hildenborough

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate 209573 DVU0627 phosphotransbutyrylase

Query= curated2:Q9X448
         (316 letters)



>lcl|MicrobesOnline__882:209573 DVU0627 phosphotransbutyrylase
          Length = 343

 Score =  198 bits (503), Expect = 2e-55
 Identities = 119/313 (38%), Positives = 179/313 (57%), Gaps = 10/313 (3%)

Query: 7   AQPSKYDRLIAAA-RAEAPAVTIVAHPCDETSLGGAIEAAEMGLITPILVAPEAKIRNVA 65
           A P   D ++AA  R   P    VA   +  +L   +EA +MG+  P+LV   A   ++A
Sbjct: 30  AAPRTLDDIVAAVVRRGIPVRVAVAACAEPNALAAVLEARDMGMAVPVLVGDIAATESIA 89

Query: 66  AEHRLDLGRREIVDVPHSHAAAAKAVALIREGRGELLMKGSLHTDELMHEVAASATGLRT 125
            E  L L   E+ D P    A  +AV  +R G  ++LMKG ++TD L+  V    +GL  
Sbjct: 90  TERGLSLEGCEVEDEPVPVKAVQRAVDRVRTGGADVLMKGLVNTDVLLRVVLNRVSGLSA 149

Query: 126 QRRISHVFVMDVPG--------HTDTLFITDAAINIFPDLEAKRDIVQNAIDLWVAIGLG 177
              +SHV V  +P          +  + ITDAA+NI P++E K  IV+NAI +  ++G+ 
Sbjct: 150 GGLLSHVAVCSLPATCGGEASASSRLVCITDAAVNISPNMERKLGIVRNAICVARSLGIP 209

Query: 178 EPRVAILSAVETVTAK-IPSTIEAAALCKMAERGQITGGVLEGPLAFDNAIDQEAARIKG 236
            PRVA+L+A E V    +P+T++A  + +MA++G+    ++ GP+A D AI  + A  KG
Sbjct: 210 SPRVAMLAATEKVMLPAMPATLDAQIVARMADQGEFGDAMVAGPMALDVAISPDIAARKG 269

Query: 237 INSPVAGHAQILVVPDLEAGNMLAKNLTFLTHADAAGLVLGARVPIVLTSRADSVRTRLA 296
           ++ PVAG A IL  PD+E+GN+L K+LT L H + AG++ G   P+V+ SR DS R++L 
Sbjct: 270 VSHPVAGRADILCAPDIESGNILYKSLTTLAHVEMAGILTGTTAPVVVPSRGDSRRSKLL 329

Query: 297 SCAVAALYAARRR 309
           S A+AA  A   R
Sbjct: 330 SLALAAYVAMECR 342


Lambda     K      H
   0.320    0.133    0.376 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 224
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 316
Length of database: 343
Length adjustment: 28
Effective length of query: 288
Effective length of database: 315
Effective search space:    90720
Effective search space used:    90720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory